From 21c325106639365900c266f705b2fd4be397fe6e Mon Sep 17 00:00:00 2001
From: Meng Li <34143965+Meng6@users.noreply.github.com>
Date: Wed, 29 Jul 2020 15:25:26 -0400
Subject: [PATCH] Delete mystudy.snakefile and add all rules to
 models.snakefile

---
 Snakefile               |  1 -
 rules/models.snakefile  | 36 ++++++++++++++++++++++++++++++++++++
 rules/mystudy.snakefile | 35 -----------------------------------
 3 files changed, 36 insertions(+), 36 deletions(-)
 delete mode 100644 rules/mystudy.snakefile

diff --git a/Snakefile b/Snakefile
index 1fbb03db..1360dcb2 100644
--- a/Snakefile
+++ b/Snakefile
@@ -4,7 +4,6 @@ include: "rules/preprocessing.snakefile"
 include: "rules/features.snakefile"
 include: "rules/models.snakefile"
 include: "rules/reports.snakefile"
-include: "rules/mystudy.snakefile" # You can add snakfiles with rules tailored to your project
 
 import itertools
 
diff --git a/rules/models.snakefile b/rules/models.snakefile
index 36eb584b..e8cd6dc6 100644
--- a/rules/models.snakefile
+++ b/rules/models.snakefile
@@ -1,5 +1,41 @@
 ruleorder: nan_cells_ratio_of_cleaned_features > merge_features_and_targets
 
+rule days_to_analyse:
+    input:
+        participant_info = "data/raw/{pid}/" + config["PARAMS_FOR_ANALYSIS"]["GROUNDTRUTH_TABLE"] + "_raw.csv"
+    params:
+        days_before_surgery = "{days_before_surgery}",
+        days_in_hospital = "{days_in_hospital}",
+        days_after_discharge= "{days_after_discharge}"
+    output:
+        "data/interim/{pid}/days_to_analyse_{days_before_surgery}_{days_in_hospital}_{days_after_discharge}.csv"
+    script:
+        "../src/models/select_days_to_analyse.py"
+
+rule targets:
+    input:
+        participant_info = "data/raw/{pid}/" + config["PARAMS_FOR_ANALYSIS"]["GROUNDTRUTH_TABLE"] + "_raw.csv"
+    params:
+        pid = "{pid}",
+        summarised = "{summarised}",
+        targets_ratio_threshold = config["PARAMS_FOR_ANALYSIS"]["TARGETS_RATIO_THRESHOLD"],
+        targets_value_threshold = config["PARAMS_FOR_ANALYSIS"]["TARGETS_VALUE_THRESHOLD"]
+    output:
+        "data/processed/{pid}/targets_{summarised}.csv"
+    script:
+        "../src/models/targets.py"
+
+rule demographic_features:
+    input:
+        participant_info = "data/raw/{pid}/" + config["PARAMS_FOR_ANALYSIS"]["GROUNDTRUTH_TABLE"] + "_raw.csv"
+    params:
+        pid = "{pid}",
+        features = config["PARAMS_FOR_ANALYSIS"]["DEMOGRAPHIC_FEATURES"]
+    output:
+        "data/processed/{pid}/demographic_features.csv"
+    script:
+        "../src/features/demographic_features.py"
+
 def input_merge_features_of_single_participant(wildcards):
     if wildcards.source == "phone_fitbit_features":
         return expand("data/processed/{pid}/{features}_{day_segment}.csv", pid=wildcards.pid, features=config["PARAMS_FOR_ANALYSIS"]["PHONE_FEATURES"] + config["PARAMS_FOR_ANALYSIS"]["FITBIT_FEATURES"], day_segment=wildcards.day_segment)
diff --git a/rules/mystudy.snakefile b/rules/mystudy.snakefile
deleted file mode 100644
index 30e2a90f..00000000
--- a/rules/mystudy.snakefile
+++ /dev/null
@@ -1,35 +0,0 @@
-rule days_to_analyse:
-    input:
-        participant_info = "data/raw/{pid}/" + config["PARAMS_FOR_ANALYSIS"]["GROUNDTRUTH_TABLE"] + "_raw.csv"
-    params:
-        days_before_surgery = "{days_before_surgery}",
-        days_in_hospital = "{days_in_hospital}",
-        days_after_discharge= "{days_after_discharge}"
-    output:
-        "data/interim/{pid}/days_to_analyse_{days_before_surgery}_{days_in_hospital}_{days_after_discharge}.csv"
-    script:
-        "../src/models/select_days_to_analyse.py"
-
-rule targets:
-    input:
-        participant_info = "data/raw/{pid}/" + config["PARAMS_FOR_ANALYSIS"]["GROUNDTRUTH_TABLE"] + "_raw.csv"
-    params:
-        pid = "{pid}",
-        summarised = "{summarised}",
-        targets_ratio_threshold = config["PARAMS_FOR_ANALYSIS"]["TARGETS_RATIO_THRESHOLD"],
-        targets_value_threshold = config["PARAMS_FOR_ANALYSIS"]["TARGETS_VALUE_THRESHOLD"]
-    output:
-        "data/processed/{pid}/targets_{summarised}.csv"
-    script:
-        "../src/models/targets.py"
-
-rule demographic_features:
-    input:
-        participant_info = "data/raw/{pid}/" + config["PARAMS_FOR_ANALYSIS"]["GROUNDTRUTH_TABLE"] + "_raw.csv"
-    params:
-        pid = "{pid}",
-        features = config["PARAMS_FOR_ANALYSIS"]["DEMOGRAPHIC_FEATURES"]
-    output:
-        "data/processed/{pid}/demographic_features.csv"
-    script:
-        "../src/features/demographic_features.py"